An RPC plugin for Cytoscape RPC that allows XML-RPC clients to query and change attributes in Cytoscape. This makes it possible to use Cytoscape as an external visualization platform without constantly in- and exporting data.

Data Analysis Framework that enables any computer program (i.e proteomics tools) to run on a Distributed Computing environment (Grid, Cloud, Cluster, Lightpath etc.). DAF provides Web Services to the end user.

Automatically recognizing concepts in human-readable text. This project uses Peregrine as text indexer. It searches for known terms in an input text and maps them to concepts in an ontology. If a term could refer to more than one concept then Peregrine tries to disambiguate it.

DEmARC is an R package for hierarchical classification of viral genomes based on multiple alignments of strongly conserved proteins. Classification is typically done on the virus family level, and quantitative support is given for both the ranks and the taxa of the classification. Different types of plots are provided for visual inspection and interpretation of the results. The methodology might be useful for the analysis of cellular organisms as well.

involves building a model infrastructure for the Dutch Biobank community, BBMRI-NL, that manages resources for the future of biomedical research. It forms a hub in the European Biobanking and Biomolecular Resources Research Infrastructure.

High-throughput analysis of genome-wide transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next generation sequencing approaches, e.g. Tn-seq, INseq and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per gene or per mutant. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data.
To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher.
We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS markedly improve the sensitivity and specificity of predicted gene essentiality.

Project for the setup of a foundation for the governance of open source software in a bioinformatics context; software that is not used by programmers; software for which the governance requires a community of users (life-scientists, biologists, clinicians, laboratory personnel, etc) as well as a community of programmers (bioinformaticians, informaticians, statisticians, etc)

An easy-to-use webserver that analyses the structural effects of protein point mutations. Project HOPE collects and combines available information from a series of webservers and databases to produce a mutation report complete with results, figures and animations.

Container of several different time alignment algorithms developed for LC-MS such as Correlation Optimized Warping, Dynamic Time Warping and Parametric Time Warping using preselected mass traces with COmponent Detection Algorithm (COW-CODA, DTW-CODA and PTW-CODA).

A web based user interface ("Knowledge Enhancer") using semantic technology to create a popup in the browser linking terms in the text to concepts in the ConceptWiki and other third party services. Aimed at knowledge discovery.

MaRIboES is a system for metabolite and reaction inference based on enzyme specificities. It employs structural and stereochemistry similarity measures and molecular fingerprints to generalise enzymatic reactions based on data available in BRENDA.

MaxAPC takes as input IMPUTE/SNPTEST .gen and .sample files. On the basis of these two file statistics are calculated and provided in the two outputfiles:
1.) the maximum, average, posterior call averaged per individual (one average per individual) - .pi file.
2.) the maximum, average, posterior call averaged per SNP (one average per SNP) - .ps file.

This application is officially programmed to up-load human metabolic pathway data from KEGG, Reactome, HumanCyc, and WikiPathways to a data warehouse. Such a data warehouse can be used to compare data across the uploaded databases. This way high similar reactions can be retrieved. Such results can offer a valuable source for a reconciliation of metabolic pathway data. A unified data model has been used that treats extracted data from any metabolic pathway database equally. Therefore addition of new metabolic pathway data is relatively easy.

Quickly and automatically generate databases and rich user interfaces to track and trace all your research data. Integrate with your analysis tools in R, Java and web services. See http://www.molgenis.org/ for more details.

Overlapping Peak Finder is a Java program that deconvolutes overlapping isotopic clusters based on an isotopic distribution prediction algorithm.
It can be used as a post-processing tool to correct the results obtained by common quantification software.

Panter stands for the Persons and Address Informationsystem NTR. Panter provides a user interface to the address and research administration database of the Netherlands Twin Register. The application is written in C# and uses an MS-SQL server as database store. An open source edition is provided here under the GPLv3 license.

PhenoLink allows linking phenotypes to large ~omics data sets, which is essential for generating leads to understand the underlying mechanism of a phenotype. It pre-processes input data to decrease noise and uses the Random Forest algorithm for feature selection to accurately find features that are linked to phenotypes. Additionally, the PhenoLink provides visualization of links that allows quick identification of relations (i) between features and phenotypes, (ii) among features, (iii) among phenotypes, and (iv) features and organisms, which use different feature sets to exhibit the same phenotype.

Time alignment for complex LC-MS datasets typically obtained from inter-laboratory studies. The developed application allows retention time alignment of diverse LC-MS datasets by first accurately identifying peak correspondences using Bi-variate 2D Kernel density estimation and then extracting a non-linear monotonic regression function from the retention time co-ordinates of these peak correspondences.